Biology subjects

Tsuda, Y.

Publications and source records attributed to Tsuda, Y..

11 recordsLinked to original sources

bioRxiv2026

Avian uropygial secretions as a novel bioinsecticide for mosquito vector control

Background: Malaria control relies heavily on interventions targeting mosquito vectors, but the rapid emergence of insecticide resistance threatens the effectiveness of existing approaches. Identifying novel, effective, and environmentally sustainable insecticides is therefore a priority. Birds produce uropygial secretions with well-documented antimicrobial properties, but their potential insecticidal activity against mosquitoes, including malaria vectors, remains unexplored. Methods: We evaluated the insecticidal activity of uropygial secretions from wild house sparrows (Passer domesticus) against the malaria vector Anopheles stephensi and four additional mosquito species of medical importance (Aedes aegypti, Aedes albopictus, Culex pipiens, and Culiseta longiareolata). A total of 2,293 adult mosquitoes were tested using CDC bottle bioassays at three secretion concentrations (0.5, 0.25, and 0.125) and an untreated control. Mosquito mortality was monitored for 120 min. Results: Uropygial secretions caused substantial mosquito knockdown/mortality, with effects increasing with concentration and exposure time. Susceptibility differed significantly among species after 120 min. Notably, An. stephensi was particularly susceptible, reaching knockdown/mortality of 92%, 94%, and 83% at 0.5, 0.25, and 0.125 concentrations, respectively. Conclusions: Our findings provide the first experimental evidence that avian uropygial secretions possess direct insecticidal activity against mosquitoes and identify them as a previously overlooked source of naturally derived insecticidal compounds. The high susceptibility of An. stephensi highlights their potential relevance for developing novel bioinsecticides for malaria vector control.

ecology↗

bioRxiv2026

VicMAG, an open-source tool for visualizing circular metagenome-assembled genomes highlighting bacterial virulence and antimicrobial resistance

Bacterial pathogens spread in clinical and environmental settings, and mobile genetic elements (MGEs), such as plasmids and phages, mediate the transfer of virulence factor genes (VFGs) and antimicrobial resistance genes (ARGs) among bacterial communities. Metagenomic analysis of environmental and wastewater samples using highly accurate long-read sequencing technologies, such as PacBio HiFi sequencing, provides valuable insights into monitoring the regional spread of VFGs and ARGs, including dissemination mediated by MGEs. No visualization tool is currently available for the comprehensive display of numerous resulting circular metagenome-assembled genomes (cMAGs) with functional gene annotations. Here, we developed VicMAG, a visualization tool for highly complex cMAGs derived from long-read metagenome assemblies annotated using updated databases of VFGs, ARGs, and MGEs. Using 353 cMAGs from PacBio HiFi sequencing of a wastewater sample, we demonstrated the utility of VicMAG for metagenome visualization. VicMAG provides comprehensive, size-aware visualization of cMAGs representing bacterial chromosomes and plasmids, annotated with VFGs, ARGs, and phages. By simultaneously visualizing all cMAGs in a framework, VicMAG facilitates a holistic understanding of the distribution and genomic context of VFGs and ARGs across complex microbial communities. This tool supports integrated surveillance of bacteria associated with virulence and antimicrobial resistance across clinical, environmental, and One Health contexts.

bioinformatics↗

bioRxiv2026

Tracing the emergence of the novel fluoroquinolone resistance gene qrtA in enterococci through environmental reservoirs and pELF-type linear plasmids

As animal hosts adapted to land, Enterococcus species diverged from a common ancestor shared with Vagococcus species by acquiring genes essential for survival and transmission in the exposed arid environment. In addition to their intrinsic ruggedness, human-associated enterococci now frequently exhibit multidrug resistance, largely driven by the accumulation of antimicrobial resistance genes (ARGs) on mobile genetic elements (MGEs). However, the source of these resistance elements, their diversity in natural reservoirs, and the risk that they pose remain unclear. To investigate the movement of novel ARGs from the environmental reservoir and the elements that convey them into clinically important enterococcal lineages, we examined environmental vancomycin-resistant enterococci (VRE) circulating in a polluted urban river in Hanoi, Vietnam. Whole-genome sequencing of VRE isolates revealed multidrug-resistance pELF-type linear plasmids harboring a novel fluoroquinolone resistance gene (qrtA) encoding a major facilitator superfamily transporter. The qrtA gene appears to have originated on Vagococcus chromosomes and to have been mobilized by IS1216E-associated MGEs. Vagococcus genomes show strong associations between ARGs, IS1216E, and plasmids related to those in enterococci, and conjugation experiments demonstrated that pELF-type linear plasmids can transfer between Enterococcus and Vagococcus without major fitness costs, positioning them as plausible vehicles for importing environmental ARGs into enterococci. Reconstruction of pELF-type linear plasmid evolution in the environment, together with database mining of rare qrtA-positive clinical isolates from Asia and Europe, suggests that qrtA-bearing pELF-type linear plasmids are in an early phase of global dissemination. These findings highlight the need for coordinated international One Health surveillance of ARG and MGE dynamics, including emerging determinants such as qrtA, together with proactive interventions to limit their spread.

microbiology↗

bioRxiv2025

Evolutionary Trade-off Between Stomatal Defense and Gas Exchange in Brassicaceae

Stomatal opening is crucial for gas exchange, but it unavoidably offers invasion by pathogens. In response, plants close stomata to prevent pathogen entry, while the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto) produces coronatine (COR), a jasmonate (JA) mimic, to counteract this plant response. Here, we demonstrate that by COR, Pto exploits CYP707A1 activation in Arabidopsis thaliana, encoding an enzyme that degrades abscisic acid, essential for stomatal closure. Notably, COR-induction of CYP707A1 is absent in other Brassicaceae species, such as Capsella rubella and Eutrema salsugineum, rendering them resistant to Pto invasion. In contrast, in A. thaliana, CYP707A1 enables rapid stomatal opening at dawn in a JA-dependent manner, enhancing gas exchange and chlorophyll content, unlike C. rubella and E. salsugineum. Promoter-swap experiments confirm that the regulatory region of CYP707A1 underlies these evolutionary diversifications. Together, our study presents a mechanism underlying an evolutionary trade-off between stomatal defense and gas exchange.

plant biology↗

bioRxiv2024

INCOMPATIBILITY GROUPS OF PSEUDOMONAS PLASMIDS REVISITED: COMPREHENSIVE ANALYSIS OF R-FACTORS AND THEIR REPLICONS

Plasmids are the most influential engines of bacterial evolution and horizontal gene transfer, fueling the global spread of traits such as antimicrobial resistance. Their deep evolutionary relationships, however, remain difficult to resolve because current classification schemes are constrained by host range and nucleotide similarity. Replication initiation proteins (RIPs), which govern plasmid persistence and diversification, also remain poorly annotated across public databases. Here we establish PInc, a curated and experimentally grounded replicon classification framework anchored in historically defined incompatibility groups of Pseudomonas plasmids. Homology searches beyond PInc revealed that most replication initiators analyzed here share a conserved winged-helix (WH) domain, defining a broad WH RIP superfamily. Using the conserved WH region, we reconstructed a large-scale phylogeny that linked WH RIPs to over 100,000 plasmids, representing approximately half of those analyzed across public databases. This phylogeny resolved eight major clades and the deep split between the single- and double-winged-helix superclades, while revealing clade-specific host and environmental distributions and substantial RIP diversity not captured by current typing tools or annotation schemes. Together, these results overcome the historical host bias of plasmid typing and provide a replication-centered view of plasmid diversification across bacterial lineages and environments.

microbiology↗

bioRxiv2024

Characterization of severe fever with thrombocytopenia syndrome virus Japanese isolate YG1 strain quasispecies using reverse genetics approaches

Three amino acid mutations have been identified in the isolated YG1 strain of severe fever thrombocytopenia syndrome virus (SFTSV), Gn (Y328H) accounts for 26.9% of the virus in patients blood, Gc (R624W) and L (N1891K) those are minor. To investigate viral properties caused by each mutation, we rescued viruses with one-three mutations. Mutations Y328H and R624W in GP increased the cell fusion activity and plaque size. Theses enhancement was more pronounced for both Y328H and R624W. The pseudotyped vesicular stomatitis virus coated with the SFTSV GP Y328H mutant showed lower infectivity in Vero E6 cells, which was compensated for by the additional R624W mutation. In the process of adaptation for virus with Y328H, the R624W mutation may be acquired. Moreover, only the viruses with the N1891K mutation in L showed significant CPE and the CPE was inhibited by the pan-caspase inhibitor, suggesting that caspase-dependent cell death occurred. Programmed cell death associated molecules caspase-1 and caspase-3 were induced in both CPE inducing and wild-type virus-infected cells. Furthermore, infection with the wild-type virus suppressed actinomycin D-induced cell death. These results suggest that SFTSV infected cells initiate programmed cell death, whereas wildt-ype virus may inhibit cell death. Furthermore, the N1891K mutation in L virus was outcompeted by a 10-fold less wild-type virus in Vero E6 cells indicating that it was not advantageous for viral survival in Vero E6 cells. Thus the quasispecies composition of SFTSV appeared to be influenced by propagative environment. ImportanceThis study shows information on viral pathogenesis by analyzing quasispecies derived from one fatal case of severe fever with thrombocytopenia syndrome virus (SFTSV) infection. Observation with recombinant SFTSV altered Gn and Gc suggests that combining mutations may increase the viability of mutant viruses, selecting viruses to create a suitable population for propagation. The N1891K mutation in L protein of SFTSV was related to CPE appearance. On the other hand, wild-type virus which is major population in patient infection was suppressive for cell death. It was suggested that SFTSV has a mechanism to escape cell death for the prolonged viral propagation in infected cells. Although the mechanism is still unknown, it has been suggested that RNA virus polymerase might be involved in the regulation of cell death. This study proposed the mechanism underlying the adaptation to the environment and survival of virus as quasispecies.

microbiology↗

bioRxiv2023

The latitudinal trend in genetic diversity and distinctiveness of Quercus robur rear edge forest remnants calls for new conservation priorities

Knowledge of the spatial distribution of intraspecific genetic variation is essential for planning conservation actions, designing networks of protected areas, and informing possible assisted migration strategies. Although the Italian peninsula harbours unique genetic variation as a legacy of Quaternary migrations, only sporadic genetic information is available for forest tree species. Here, we present the first geographically comprehensive genetic characterisation of Quercus robur, an iconic broadleaved species of European floodplain forests, in an area which acted as a primary glacial refugium for the species. 745 individuals from 25 populations were sampled and genotyped with 16 microsatellite markers. Their genetic structure was assessed through various metrics of diversity and distinctiveness, as well as by Bayesian clustering and multivariate methods. The demographic history of inferred gene pools was evaluated through Approximate Bayesian Computation analysis. Genetic distinctiveness showed a decline with increasing latitude, while allelic richness reached its peak in central Italy. A south-to-north trend in the complexity of the genetic structure was observed, with peninsular Italy being characterised by intermingled gene pools in contrast to the relative homogeneity exhibited by northern populations. Demographic inference indicated that the southern gene pool has been genetically isolated since the penultimate interglacial, whereas populations from central Italy persisted locally in a mosaic of small refugia during the last glaciation. Our results brought out the complexity of the genetic structure of forest trees populations in southern Europe. At least three Q. robur refugia contributed to the genetic layout of extant populations after the last glacial period, but refugial areas were probably even more numerous in central Italy. Such a detailed characterization sheds new light on the priorities to be established for the conservation of highly fragmented Q. robur populations in an area rich in diversified genetic lineages.

genetics↗

bioRxiv2021

Dissecting the co-transcriptome landscape of plants and microbiota members

Interactions between plants and neighboring microbial species are fundamental elements that collectively determine the structure and function of the plant microbiota. However, the molecular basis of such interactions is poorly characterized. Here, we monocolonized Arabidopsis leaves with nine plant- associated bacteria from all major phyla of the plant microbiota and profiled co- transcriptomes of plants and bacteria. We detected both common and distinct co- transcriptome signatures among plant-commensal pairs. In planta responses of commensals were similar to those of a disarmed pathogen characterized by the suppression of genes involved in general metabolism in contrast to a virulent pathogen. We identified genes that are enriched in the genome of plant-associated bacteria and induced in planta, which may be instrumental for bacterial adaptation to the host environment and niche separation. This study provides insights into how plants discriminate among bacterial strains and lays the foundation for in- depth mechanistic dissection of plant-microbiota interactions.

plant biology↗

bioRxiv2020

CTDSP1 inhibitor rabeprazole regulates DNA-PKcs dependent topoisomerase I degradation and irinotecan drug resistance in colorectal cancer

Irinotecan specifically targets topoisomerase I (topoI), and is used to treat various solid tumors, but only 13-32% of patients respond to the therapy. Now, it is understood that the rapid rate of topoI degradation in response to irinotecan causes irinotecan resistance. We have published that the deregulated DNA-PKcs kinase cascade ensures rapid degradation of topoI and is at the core of the drug resistance mechanism of topoI inhibitors, including irinotecan. We also identified CTD small phosphatase 1 (CTDSP1) (a nuclear phosphatase) as a primary upstream regulator of DNA-PKcs in response to topoI inhibitors. Previous reports showed that rabeprazole, a proton pump inhibitor (PPI) inhibits CTDSP1 activity. The purpose of this study was to confirm the effects of rabeprazole on CTDSP1 activity and its impact on colon cancer. Using HCT116 and HT29, with high and low CTDSP1 expression respectively and a retrospective analysis of patients receiving irinotecan with or without rabeprazole have indicated the effect of CTDSP1 in irinotecan response. These results indicate that CTDSP1 promotes sensitivity to irinotecan and rabeprazole prevents this effect, resulting in drug resistance. To ensure the best chance at effective treatment, rabeprazole may not be a suitable PPI for cancer patients treated with irinotecan.

cancer biology↗

bioRxiv2019

In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions

Understanding how gene expression is regulated in plant pathogens is crucial for pest control and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a foliar bacterial pathogen, Pseudomonas syringae, in Arabidopsis thaliana and identified a number of bacterial processes influenced by plant immunity at the mRNA and the protein level. We found instances of both concordant and discordant regulation of bacterial mRNAs and proteins. Notably, the tip component of bacterial type III secretion system was selectively suppressed by the plant salicylic acid pathway at the protein level, suggesting protein-level targeting of the bacterial virulence system by plant immunity. Furthermore, gene co-expression analysis illuminated previously unknown gene regulatory modules underlying bacterial virulence and their regulatory hierarchy. Collectively, the integrated in planta bacterial omics approach provides molecular insights into multiple layers of bacterial gene regulation that contribute to bacterial growth in planta and elucidate the role of plant immunity in controlling pathogens.

plant biology↗

bioRxiv2019

Genetic analysis of Aedes aegypti captured in two international airports serving the Greater Tokyo area during 2012-2015

Introduction of exotic diseases vectors into a new habitat can drastically change the local epidemiological situation. During 2012--2015, larvae and an adult of the yellow-fever mosquito, Aedes aegypti, were captured alive in two international airports serving to the Greater Tokyo Area, Japan. Because this species does not naturally distribute in this country, those mosquitoes were considered to be introduced from oversea via air-transportation. To infer the places of origin of those mosquitoes, we genotyped 12 microsatellite loci for which the most comprehensive population genetic reference is available. Although clustering by Bayesian and multivariate methods both suggested all those airport mosquitoes belong to Asia/Pacific population, they were not clustered into a single population. Also, there was variation in mitochondrial Cox1 haplotypes among mosquitoes collected in different incidents of discovery which indicated the existence of multiple maternal origins. Whereas we conclude there is little evidence to support overwintering of Ae. aegypti in the airports in this study, special attention is still desired to prevent the invasion of this prominent arbovirus vector.

genetics↗